crossing96/oncoscreening huggingface dataset:
Comprehensive Characterization of Common and Cancer-Specific Differently Expressed lncRNAs in Urologic Cancers.	Urologic cancers, comprising prostate carcinoma (PCa), renal cell carcinoma (RCC), and bladder carcinoma (BCa), were the commonly occurred carcinoma amid males. Long noncoding RNAs (lncRNAs) with the length of more than 200 nt functioned importantly in physiological and pathological advancement. Nevertheless, further investigation regarding lncRNA expression feature and function in urologic cancers should be essential. This study is aimed at uncovering the roles of the differently expressed lncRNAs in urologic cancers. The data of gene expression levels was downloaded from lncRNAtor datasets. The lncRNA expression pattern existing in different urologic cancers was assessed by hierarchical clustering analysis. Gene Ontology (GO) analysis and KEGG pathway analysis were separately applied to evaluate the biological function and process and the biological pathways involving differently expressed lncRNAs. Our results indicated that 18 lncRNA expressions were increased, and 16 lncRNA expressions were reduced in urologic cancers after comparison with that in normal tissues. Moreover, our results demonstrated 61, 422, 137, and 281 lncRNAs were specifically dysregulated in bladder cancer (BLCA), kidney renal clear cell cancer (KIRC), kidney renal papillary cell cancer (KIRP), and prostate adenocarcinoma (PRAD), respectively. Bioinformatics analysis showed that differently expressed lncRNAs displayed crucially in urologic cancers. The prognostic value of common and cancer-specific differently expressed lncRNAs, such as PVT1, in cancer outcomes, was emphasized here. Our research has deeply unearthed the mechanism of differently expressed lncRNAs in urologic cancers development.	bladder
The effect of tumor grade heterogeneity on recurrence in non-muscle invasive bladder cancer.	OBJECTIVE: To investigate the outcomes of mixed-grade non-muscle invasive bladder cancer (NMIBC) based on the degree of high-grade predominance. METHODS: We identified patients in our institutional database who had a transurethral resection of bladder tumor(s) for NMIBC. Tumors with mixed-grade features on pathology report were reanalyzed, assigned the percentage high-grade component, and stratified into ≤ 5% high-grade and > 5% high-grade groups. All others were classified as low-grade or high-grade NMIBC. Differences in recurrence-free survival were assessed by log-rank test. A multivariable Cox regression model was used to evaluate the impact of tumor grade on recurrence, controlling for tumor stage, size, multifocality, and intravesical therapy. RESULTS: Two hundred and twenty patients were followed for a median of 2 years; 127 (58%) had low-grade NMIBC, 66 (30%) had high-grade NMIBC, and 27 (12%) had mixed-grade NMIBC. Of the mixed-grade patients, 14 had a ≤ 5% high-grade component, and 13 had a > 5% high-grade component. Recurrence rates across all groups ranged from 42% to 79%. There was no significant difference in intravesical recurrence-free survival among the grade categories as assessed by log-rank test. On multivariable Cox regression analysis, grade category was not significantly associated with likelihood of recurrence. CONCLUSIONS: The prognosis of mixed-grade histology in NMIBC has not previously been well defined. Although grade category was not found to be an independent significant predictor of recurrence, the recurrence rate for mixed-grade tumors was quite high overall. Further studies are required to better understand appropriate risk stratification and treatment of mixed-grade NMIBC.	bladder
Does minimally invasive surgery for bladder cancer result in unusual sites of metastasis?	BACKGROUND: To compare sites of metastasis for the laparoscopic (LRC) and open (ORC) approaches in a cohort of patients at a district general hospital. Morbidity and mortality for the two approaches are assessed using secondary outcomes of length of stay and complication rate. Metastasis rate and site are compared. METHODS: A retrospective case note review was carried out for all patients who underwent cystectomy for bladder malignancy at Pinderfields General Hospital, Wakefield between 2010 and 2016 (n = 219). There were 150 males and 69 females in 107 minimally invasive cases and 87 open (missing data on 25 cases). Data were analysed using Microsoft Excel XLSTAT. RESULTS: Recurrence rate was 25.1% and did not differ significantly with approach (p = 0.89). Sites of recurrence did not differ with operative approach, the most frequent being pelvis, chest and bone. Unusual sites of recurrence included abdominal wall and sigmoid colon which both occurred in LRC. Length of stay was greater for the open approach (median LRC = 10, ORC = 13, p < 0.01). Five-year survival was 74.9%. Survival distribution did not significantly differ with operative approach (p = 0.43), and there was no significant association between operative approach and patient death within the follow-up period (p = 0.09). Stricture rate was 4.1% and was not significantly different between the 2 groups (p = 0.29). Median time to stricture was 130 days. Clavien-Dindo scores for complications did not differ with approach (p = 0.93), and there was no significant association between operative approach and whether complications developed (p = 0.19). CONCLUSIONS: The adverse oncological outcomes in minimally invasive approaches suggested by some studies are not confirmed here. Those in the LRC group were discharged sooner, though this did not translate into differences in morbidity or survival. Analysis of the association between individual complications and length of stay may clarify this further. Shorter hospital stay is also likely to have significant financial implications. Despite no significant difference in outcomes, the findings demonstrate potential benefits of LRC. Extensions of this study could include: cost-benefit analysis, examination of individual complications' effect on length of stay; and analysis of approach-specific factors contributing to perioperative deaths.	bladder
The effect of race on stage at presentation and survival in upper tract urothelial carcinoma.	Background The effect of racial/ethnic group on survival in upper tract urothelial carcinoma (UTUC) is unknown. We tested this concept in non-metastatic UTUC patients treated with radical nephroureterectomy (RNU) and hypothesized that important differences may exist according to racial/ethnic groups. Material and Methods We relied on the Surveillance Epidemiology and End Results database (2004-2016). We relied on Propensity-score matching (ratio 1:4). Subsequently, cumulative incidence plots and multivariable competing risks regression models (CRR) addressed cancer-specific mortality (CSM). Results Of 9129 assessable patients, 7454 (81.7%) were Caucasian vs. 665 (7.3%) Hispanic vs. 584 (6.4%) Asian vs. 426 (4.7%) African-American. No statistically significant differences were recorded for tumor grade or T-stage, between all racial/ethnic groups. However, within patents who received lymph-node dissection (n = 2694, 29.5%), Asians exhibited the highest rate of more than 2 positive lymph nodes at RNU (19.0%, followed by 17.1% African-Americans, 15.0% Caucasians and 12.6% Hispanics, P < 0.001). After PS-matching and multivariable CRR, Asian race/ethnicity independently predicted higher CSM, relative to Caucasians (Hazard ratio: 1.29, P < 0.01). No statistically significant differences according to CSM was recorded in the remaining races/ethnicities comparisons (all P ≥ 0.1) Conclusion Important CSM differences may exist according to race/ethnicity in non-metastatic UTUC patients treated with RNU. However, these differences only apply to Asian patients, who account for 6% of the overall non-metastatic UTUC cohort treated with RNU. In consequence, in clinical practice Asian patients should be given particular attention with the intent of reducing the CSM disadvantage that cannot be clearly explained by stage and/or grade disadvantage at diagnosis.	bladder
USP24-GSDMB complex promotes bladder cancer proliferation via activation of the STAT3 pathway.	Background: Bladder cancer is the fourth and tenth most common malignancy in men and women worldwide, respectively. One of the main reasons for the unsatisfactory therapeutic control of bladder cancer is that the molecular biological mechanism of bladder cancer is complex. Gasdermin B (GSDMB) is one member of the gasdermin family and participates in the regulation of cell pyroptosis. The role of GSDMB in bladder cancer has not been studied to date. Methods: TCGA database was used to exam the clinical relevance of GSDMB. Functional assays such as MTT assay, Celigo fluorescent cell-counting assay, Annexin V-APC assay and xenografts were used to evaluate the biological role of GSDMB in bladder cancer. Mass spectrometry and immunoprecipitation were used to detect the protein interaction between GSDMB and STAT3, or GSDMB and USP24. Western blot and immunohistochemistry were used to study the relationship between USP24, GSDMB and STAT3. Results: In this study, bioinformatics analysis indicated that the mRNA expression level of GSDMB in bladder cancer tissues was higher than that in adjacent normal tissues. Then, we showed that GSDMB promoted bladder cancer progression. Furthermore, we demonstrated that GSDMB interacted with STAT3 to increase the phosphorylation of STAT3 and modulate the glucose metabolism and promote tumor growth in bladder cancer cells. Besides, we also showed that USP24 stabilized GSDMB to activate STAT3 signaling, which was blocked by the USP24 inhibitor. Conclusions: We suggested that aberrantly up-regulated GSDMB was responsible for enhancing the growth and invasion ability of bladder cancer cells. Then, we showed that GSDMB could bind to STAT3 and activate STAT3 signaling in bladder cancer. Furthermore, we also demonstrated that USP24 interacted with GSDMB and prevented GSDMB from degradation in bladder cancer cells. Therefore, the USP24/GSDMB/STAT3 axis may be a new targetable signaling pathway for bladder cancer treatment.	bladder
A 25-year perspective on evaluation and understanding of biomarkers in urologic cancers.	The past 25 years have witnessed an explosion of investigative attempts to identify clinically useful biomarkers which can have meaningful impacts for patients with urologic cancers. However, in spite of the enormous amount of research aiming to identify markers with the hope of impacting patient care, only a handful have proven to have true clinical utility. Improvements in targeted imaging, pan-omics evaluation, and genetic sequencing at the tissue and single-cell levels have yielded many potential targets for continued biomarker investigation. This article, as one in this series for the 25th Anniversary Issue of Urologic Oncology: Seminars and Original Investigations, serves to give a perspective on our progress and failures over the past quarter-century in our highest volume urologic cancers: prostate, bladder, and kidney cancers.	bladder
Construction of a novel mRNA-signature prediction model for prognosis of bladder cancer based on a statistical analysis.	BACKGROUND: Bladder cancer (BC) is a common malignancy neoplasm diagnosed in advanced stages in most cases. It is crucial to screen ideal biomarkers and construct a more accurate prognostic model than conventional clinical parameters. The aim of this research was to develop and validate an mRNA-based signature for predicting the prognosis of patients with bladder cancer. METHODS: The RNA-seq data was downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were screened in three datasets, and prognostic genes were identified from the training set of TCGA dataset. The common genes between DEGs and prognostic genes were narrowed down to six genes via Least Absolute Shrinkage and Selection Operator (LASSO) regression, and stepwise multivariate Cox regression. Then the gene-based risk score was calculated via Cox coefficient. Time-dependent receiver operating characteristic (ROC) and Kaplan-Meier (KM) survival analysis were used to assess the prognostic power of risk score. Multivariate Cox regression analysis was applied to construct a nomogram. Decision curve analysis (DCA), calibration curves, and time-dependent ROC were performed to assess the nomogram. Finally, functional enrichment of candidate genes was conducted to explore the potential biological pathways of candidate genes. RESULTS: SORBS2, GPC2, SETBP1, FGF11, APOL1, and H1-2 were screened to be correlated with the prognosis of BC patients. A nomogram was constructed based on the risk score, pathological stage, and age. Then, the calibration plots for the 1-, 3-, 5-year OS were predicted well in entire TCGA-BLCA patients. Decision curve analysis (DCA) indicated that the clinical value of the nomogram was higher than the stage model and TNM model in predicting overall survival analysis. The time-dependent ROC curves indicated that the nomogram had higher predictive accuracy than the stage model and risk score model. The AUC of nomogram time-dependent ROC was 0.763, 0.805, and 0.806 for 1-year, 3-year, and 5-year, respectively. Functional enrichment analysis of candidate genes suggested several pathways and mechanisms related to cancer. CONCLUSIONS: In this research, we developed an mRNA-based signature that incorporated clinical prognostic parameters to predict BC patient prognosis well, which may provide a novel prognosis assessment tool for clinical practice and explore several potential novel biomarkers related to the prognosis of patients with BC.	bladder
Anticancer Effects of Cinnamaldehyde Through Inhibition of ErbB2/HSF1/LDHA Pathway in 5637 Cell Line of Bladder Cancer.	BACKGROUND AND OBJECTIVE: The growing prevalence of bladder cancer worldwide has become a major concern for researchers, and the side effects of chemotherapy drugs have always been a major problem in cancer treatment. Cinnamaldehyde, the active ingredient in the Cinnamon plant, has long been considered with anti-oxidant and anti-inflammatory effects. METHODS: Bladder cancer 5637 cell lines were treated with the different concentrations of Cinnamaldehyde. MTT assay was performed to evaluate cell viability at 24, 48, and 72 hours. The concentration of 0.02, 0.04, and 0.08 mg/ml of Cinnamaldehyde was selected. Apoptosis was assessed with Annexin V-FITC/PI and Hochest33258 staining. Cell migration was performed by the scratch test. To evaluate Cinnamaldehyde effect on glycolysis, the gene expression of epidermal growth factor receptor 2 (ErbB2), Heat Shock Protein Transcription Factor-1 (HSF1) and lactate dehydrogenase A (LDHA), as well as the protein levels of HSF1 and LDHA, LDH activity and finally glucose consumption and lactate production, were measured. RESULTS: Cinnamaldehyde significantly increased apoptosis rate in the 5637 cells (p<0.05). Furthermore, it significantly reduced the gene expression of ErbB2, HSF1, and LDHA, protein level of HSF1 and LDHA, LDH activity, as well as cell migration, glucose consumption, and lactate production (p<0.05). These changes were dose-dependent. CONCLUSION: Thus, Cinnamaldehyde induced apoptosis and decreased growth in 5637 cells by reducing ErbB2-HSF1- LDHA pathway.	bladder
The role of matrix metalloproteinases in pathogenesis of human bladder cancer.	Matrix metalloproteinases (MMPs) play an important role in many physiological and pathological processes, including neoplastic processes. They belong to a group of enzymes called endopeptidases and have the ability to hydrolyze all proteins in the extracellular matrix (ECM). They are produced in most connective tissue cells, macrophages, leukocytes, endothelial cells, microglial cells and in cancer cells. Neoplastic diseases are one of the main causes of death in Poland and in the world, therefore learning about the process of carcinogenesis seems to be particularly important. The process of carcinogenesis is currently widely studied and MMPs play one of the key roles in the development of cancer. They do this by regulating local tumor growth, stromal invasion, stimulating angiogenesis and metastasis formation. Bladder cancer is the 7th most common cancer in the male population and the 11th most common cancer in the world. In bladder cancer, most studies have been devoted to MMP-2 and MMP-9, that are enzymes responsible for the degradation of type IV collagen in the first place, which through the destruction of basement membranes and ECM, play an essential role in the tumor invasion process. Since bladder cancer is characterized by the ability to relapse, from the point of view of clinical practice it seems particularly important to develop a marker of early bladder tumor recurrence. MMPs detected in the urine and serum of patients with bladder cancer are potential factors that could play such a role.	bladder
The impact of preoperative immune checkpoint inhibitors on kidney and bladder cancer surgeries: a systematic review(☆).	Therapies based on the use of immune checkpoint inhibitors (ICIs), such as nivolumab, pembrolizumab, ipilimumab, atezolizumab, avelumab, and durvalumab, have proven effective in the treatment of metastatic urological neoplasms. Recently, it has been hypothesized that the use of this type of treatment prior to surgery could lead to an increased difficulty in renal and bladder surgeries. The literature concerning this topic, however, is still scarce and non-consensual. In our systematic review, we used the PRISMA guidelines methodology to search the pertinent literature available up to June 18, 2020 in PubMed. Additionally, we searched the related grey literature in the abstracts of the meetings of the American Society of Clinical Oncology (ASCO), American Society of Clinical Oncology Genitourinary (ASCO-GU), European Society of Medical Oncology (ESMO), and American Urological Association (AUA) from 2015 to 2020. We were able to find only 16 publications that addressed the use of ICIs prior to surgery in kidney and bladder neoplasms. The results were conflicting, and usually the issue of surgical difficulties after the use of ICIs was not directly approached. We hope that our publication may raise the awareness towards the need to further investigate the effects of neoadjuvant ICIs on surgical outcomes in urologic cancers.	bladder
Laparoscopic compared with open nephroureterectomy in upper urinary tract urothelial carcinoma: A systemic review and a meta-analysis.	BACKGROUND: We performed a meta-analysis to evaluate the effects of open nephroureterectomy compared with laparoscopic nephroureterectomy on postoperative results in upper urinary tract urothelial carcinoma subjects. METHODS: A systematic literature search up to January 2021 was done and 36 studies included 23 013 subjects with upper urinary tract urothelial carcinoma at the start of the study; 8178 of them were laparoscopic nephroureterectomy, and 14 835 of them were open nephroureterectomy. They were reporting relationships between the efficacy and safety of open nephroureterectomy compared with laparoscopic nephroureterectomy in the treatment of upper urinary tract urothelial carcinoma. We calculated the odds ratio (OR) or the mean difference (MD) with 95% confidence intervals (CIs) to assess the efficacy and safety of open nephroureterectomy compared with laparoscopic nephroureterectomy in the treatment of upper urinary tract urothelial carcinoma using the dichotomous or continuous method with a random or fixed-effect model. RESULTS: Laparoscopic nephroureterectomy in subjects with upper urinary tract urothelial carcinoma was significantly related to longer operation time (MD, 43.90; 95% CI, 20.91-66.90, P < .001), shorter hospital stay (MD, -1.71; 95% CI, -2.42 to -1.00, P < .001), lower blood loss (MD, -133.82; 95% CI, -220.92 to -46.73, P = .003), lower transfusion need (OR, 0.56; 95% CI, 0.47-0.67, P < .001) and lower overall complication (OR, 0.79; 95% CI, 0.70-0.90, P < .001) compared with open nephroureterectomy. However, no significant difference was found between laparoscopic nephroureterectomy and open nephroureterectomy in subjects with upper urinary tract urothelial carcinoma in 2-5-years recurrence-free survival (OR, 0.90; 95% CI, 0.69-1.18, P = .46), 2-5-years cancer-specific survival (OR, 0.94; 95% CI, 0.69-1.28, P = .68) and 2-5-years overall survival (OR, 1.31; 95% CI, 0.91-1.87, P = .15). CONCLUSIONS: Laparoscopic nephroureterectomy in subjects with upper urinary tract urothelial carcinoma may have a longer operation time, shorter hospital stay, lower blood loss, transfusion need and overall complication compared with open nephroureterectomy. Further studies are required to validate these findings.	bladder
Oxidative stress parameters as biomarkers of bladder cancer development and progression.	The epidemiological studies confirm that the overproduction of free radical is an important factor of cancer induction as well as development, and loss of antioxidant systems efficiency is associated with an increased risk of carcinogenesis. While bladder cancer is the fourth most common type of cancer all over the world, there is little evidence of the advancing changes in oxidative/nitrative stress during the progression of bladder cancer. Our study aimed to investigate the plasma levels of typical markers of oxidative/nitrative stress depending on the clinical classification of bladder cancer differentiation and infiltration degree. We examined 40 patients with newly diagnosed bladder cancer and 20 healthy volunteers as a control group. We analysed the plasma levels of protein carbonyls, thiol groups, 3-nitrotyrosine, lipid peroxidation, as well as non-enzymatic plasma antioxidant capacity using DPPH(·) and ABTS(·+) radicals. We confirmed that all analysed biomarkers are higher in enrolled BC patients than in healthy subjects. Furthermore, our findings demonstrate a positive correlation between the degree of bladder cancer progression and the level of oxidative stress, but no correlation in the case of NT-3. Based on obtained results, we might conclude that during carcinogenesis of the bladder increased oxidative damage of biomolecules is manifested. This indicates the participation of oxidative stress in the development of bladder cancer, and it is important the ensure the proper antioxidant protection.	bladder
Tumor Escape Phenotype in Bladder Cancer Is Associated with Loss of HLA Class I Expression, T-Cell Exclusion and Stromal Changes.	Cancer eradication and clinical outcome of immunotherapy depend on tumor cell immunogenicity, including HLA class I (HLA-I) and PD-L1 expression on malignant cells, and on the characteristics of the tumor microenvironment, such as tumor immune infiltration and stromal reaction. Loss of tumor HLA-I is a common mechanism of immune escape from cytotoxic T lymphocytes and is linked to cancer progression and resistance to immunotherapy with the inhibitors of PD-L1/PD-1 signaling. Here we observed that HLA-I loss in bladder tumors is associated with T cell exclusion and tumor encapsulation with stromal elements rich in FAP-positive cells. In addition, PD-L1 upregulation in HLA-I negative tumors demonstrated a correlation with high tumor grade and worse overall- and cancer-specific survival of the patients. These changes define common immuno-morphological signatures compatible with cancer immune escape and acquired resistance to therapeutic interventions across different types of malignancy. They also may contribute to the search of new targets for cancer treatment, such as FAP-expressing cancer-associated fibroblasts, in refractory bladder tumors.	bladder